X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5UYJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529324% PEG 3350; 0.14 M Ammonium Acetate; 0.1M CHC buffer pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.5451.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.738α = 90
b = 73.738β = 90
c = 123.883γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-11-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.979100APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1219.9496.50.0930.1050.0480.99712.28.422752
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0598.51.0020.5190.7212.18.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5UYJ219.9421613112195.540.188770.186880.22531RANDOM37.652
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
1.381.38-2.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.311
r_dihedral_angle_4_deg19.091
r_dihedral_angle_3_deg12.827
r_dihedral_angle_1_deg5.966
r_long_range_B_refined4.569
r_long_range_B_other4.568
r_scangle_other2.74
r_mcangle_it2.563
r_mcangle_other2.563
r_scbond_it1.758
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.311
r_dihedral_angle_4_deg19.091
r_dihedral_angle_3_deg12.827
r_dihedral_angle_1_deg5.966
r_long_range_B_refined4.569
r_long_range_B_other4.568
r_scangle_other2.74
r_mcangle_it2.563
r_mcangle_other2.563
r_scbond_it1.758
r_scbond_other1.758
r_mcbond_it1.62
r_mcbond_other1.608
r_angle_refined_deg1.595
r_angle_other_deg0.981
r_chiral_restr0.106
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2174
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing